Change your template to use choose instead of an if. You can use multiple when tests inside a choose and the otherwise would be the else part of an if/else if/else statement
Code:
  <xsl:template name ='IsIDPresent'>
    <xsl:param name='ID' />
    <xsl:choose>
      <xsl:when test ='//FACILITY_RELATED/PES_ID = $ID'>
        <xsl:value-of select ='$ID'/> - present
      </xsl:when>
      <xsl:otherwise>
        <xsl:value-of select ='$ID'/> - not present
      </xsl:otherwise>
    </xsl:choose>
  </xsl:template>